Aptamers are short strands of DNA or RNA with unique secondary and tertiary structures that enable highly selective binding to various types of targets. While aptamers are similar to antibodies in their ability to specifically bind with high affinity, there are some key differences between antibodies and aptamers which have prompted an increase in aptamer development projects. Several hot areas for aptamers, along with specific aptamer advantages, are outlined below.
The detection and measurement of small molecules and metabolites is an ongoing challenge in drug development, as small molecules do not elicit the immune response required for traditional antibody production. Unlike antibodies, aptamers are chemically synthesized and easily selected for binding to non-immunogenic compounds. Several groups are combining aptamers with biosensor platforms to develop fast, simple tests for detection and monitoring of small molecule drug compounds, including azole antifungal drugs, aminoglycoside antibiotics, and antiretroviral drugs (1,7). The bioanalysis of antibody-drug conjugates (ADCs) is particularly difficult, as it involves analysis of the antibody-drug complex, unconjugated antibody, unconjugated drug, and drug metabolites (6). Aptamers can be selected for each of the molecules and complexes associated with ADCs for use in a single detection platform. Read more about aptamers to small molecules.
Biomarker Discovery & Detection
Through a process known as the Sequential Evolution of Ligands by Exponential Enrichment, or SELEX, researchers elute and amplify aptamers with selective affinity for a particular target of interest. Using whole cells for aptamer selection, researchers can select for aptamers binding to a specific cell type, without targeting a known cell surface marker. Analysis of aptamers selected against whole cells has led to the discovery of several new biomarkers. (3) Learn more about Cell-SELEX and the identification of biomarkers using aptamers.
There are a number of different types of antibody-based assays and methods for measuring clinical biomarkers, but there are specific areas where aptamers present key advantages. Unlike antibodies, aptamers can be selected against toxins and small molecules. They can also be selected to distinguish between highly similar molecules, such as neurotransmitters or drug metabolites. Aptamers are also stable at elevated temperatures, making them an attractive choice for field-based assays. Once an aptamer is selected it can be chemically synthesized, a process that is highly reproducible and cost-effective, meeting important needs for long-term biomarker assay production. Aptamer use is being explored in a wide range of biomarker assays, including LFAs, biosensors, and ELISA-like assays (2). Read more about the advantages of aptamers for biomarker analysis.
One of the most exciting applications for aptamers is cell targeting. A growing number of studies have used aptamer-drug complexes to deliver drug to specific cells, lowering required dosage, increasing the effectiveness of the drug and dramatically decreasing off-target effects. Aptamers can be easily conjugated to a wide range of compounds (including siRNA, small molecule drugs, and other aptamers) without affecting their selectivity and affinity. The small size of aptamers (about 1/10th the size of an antibody) offers reduced immunogenicity and an enhanced ability to infiltrate tissues and cells (4,8). Read more about targeted drug delivery with aptamers.
In Vivo Imaging
Imaging plays a major role in the diagnosis and monitoring of disease. For some cancers, including lung cancer, pancreatic cancer, and liver cancer, earlier detection through more sensitive imaging is needed to accelerate treatment and improve outcomes (2). In an effort to increase the sensitivity of in vivo imaging, several research groups are currently working with aptamers for targeted imaging. Due to their small size, aptamers are generally non-immunogenic and penetrate tumor tissue more quickly and easily. They are chemically synthesized and easily modified for detection and enhanced in vivo stability (Read “Enhancing Aptamer Stability”). They can be selected to differentiate between highly similar compounds and conjugated to a wide range of molecules without affecting target binding. Selectivity, biocompatibility and flexibility make aptamers ideal targeting agents for in vivo imaging (10). Read more about in vivo imaging with aptamers.
Small aptamer size and the ability to conjugate aptamers without affecting selectivity or affinity are critical for biosensor development. The small size of capture aptamers enables binding events to take place close to the biosensor surface for enhanced detection. Aptamers have also been successfully immobilized on a wide range of materials. Structure-switching aptamers and fluorescent labels are easily incorporated into sensor design. The ability to select aptamers against non-immunogenic metabolites and toxic compounds creates a wide range of possibilities for monitoring and detection. In many cases, aptamers are immobilized through a thiol modification. Once sensor design is optimized, alternate thiolated aptamers can be substituted for selective detection of new targets (1,5,7). Read more about aptamer-based biosensor development.
Pull-Down / Purification
Several ongoing aptamer projects are focused on the development of aptamer-based affinity columns for the removal of high-abundance serum proteins, removal of environmental or process-related contaminants, and the purification of selective molecules. Aptamers can be selected under pH, ionic strength, and temperature conditions favorable for affinity chromatography and they are easily conjugated to chromatographic supports. Small aptamer size enables higher density and increased column capacity. High aptamer purity, batch-to-batch consistency and low-cost chemical production are important when a large quantity of material is required to purify precious material (9). The ability to re-fold aptamers may also be useful for the regeneration / re-use of affinity columns in certain applications. Read more about Aptamers in affinity purification.
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- Aliakbarinodehi, N., et al. Aptamer-based field-effect biosensor for tenofovir detection. Scientific Reports. 2017. 7:44409. doi: 10.1038/srep44409
- Jayasena, S. D. Aptamers: An emerging class of molecules that rival antibodies in diagnostics. Clinical Chemistry. 1999. 45(9):1628-1650.
- Jin, C. et al., Cancer biomarker discovery using DNA aptamers. Analyst. 2015. 10.1039/C5AN01918D.
- Lozano, T. et al. Targeting inhibition of Foxp3 by a CD28 20-Fluro oligonucleotide aptamer conjugated to P60-peptide enhances active cancer immunotherapy. Biomaterials. 2016. 91:73-80. dx.doi.org/10.1016/j.biomaterials.2016.03.007
- Pfeiffer, F. et al. Selection and biosensor application of aptamers for small molecules. Frontiers in Chemistry. 2016. 4:25.
- Saad, O.M., e al. Bioanalytical approaches for characterizing catabolism of antibody-drug conjugates. Bioanalysis. 2015. 7(13)1583-1604.
- Wiedman, G.R. et al. An aptamer-based biosensor for the azole class of antifungal drugs. mSphere. 2017. 2(4):e00274-17.
- Wu, H., et al. Novel CD123-aptamer-originated targeted drug trains for selectively delivering cytotoxic agent to tumor cells in acute myeloid leukemia theranostics. Drug Delivery. 2017. 24(1): 1216-1229
- Zhao, Q, et al. Applications of aptamer affinity chromatography. TrAC Trends in Analytical Chemistry. Dec 2012. 41:46-57. doi:org/10.1016/j.trac.2012.08.005.
- Zhang, Y. et al. Aptamer-targeted magnetic resonance imaging contrast agents and their applications. Journal of Neuroscience and Nanotechnology. 2018. 18:3759-3774.